I think this might help, although I am not sure, really: It might be worthwhile to try k, h, -l as twin operator. Does not cost anything since you figured it out in phenix anyway. Please let me know whether this worked.
Best Marius Marius Schmidt, Dr. rer. Nat. (habil.) Professor University of Wisconsin-Milwaukee Kenwood Interdisciplinary Research Complex Physics Department, Room 3087 3135 North Maryland Avenue Milwaukee, Wi 53211 phone (office): 1-414-229-4338 phone (lab): 414-229-3946 email: [email protected] https://uwm.edu/physics/people/schmidt-marius/ https://sites.uwm.edu/smarius/ https://www.bioxfel.org/ Nature News and Views: https://www.nature.com/articles/d41586-023-00504-4 ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Janani Ganesh <[email protected]> Sent: Wednesday, May 28, 2025 6:22 AM To: [email protected] <[email protected]> Subject: Re: [ccp4bb] Requesting help with twin refinement Dear Professor, Thank you for reviewing my data. Following your guidance, I have reprocessed the dataset using XDS in P32 (No. 150) space group. After completing integration, I proceeded with scaling and merging using AIMLESS. I have attached the AIMLESS log file for your review. I sincerely appreciate your continued support and valuable insights. Regards, Janani Ganesh On Wed, 28 May 2025 10:47:56 +0100, Eleanor Dodson <[email protected]> wrote: >WEll - I think this explains your crazy B values - you have somehow >*normalised* the data at processing stagr. >From the pointless log.. >You usually dont need a reference data set and certainly not a set of >calculated structure factors. >Do you have CCP4I2 installed? >If so just feed the integrated data through the processing and send me the >log perhaps? >.... >*Reference list generated by structure factor calculation* > from coordinate file >/home/janani-ganesh/Documents/JG/XData/K232Q_24042025_P72A5/CCP4I/K232Q_P72_phaser.1_refmac1.pdb >Spacegroup: P 32 2 1 >Cell: 81.84 81.84 134.77 90.00 90.00 120.00 >Maximum resolution used: 1.884 >Number of reflections: 42901 >I*ntensity normalisation: B-factor = -8.7* > >*And taken from the phenix log:* >Note that the <Fobs> at low resolution is slightly LOWER than at the >highest resolution! This is unlikely. for a protein! >..... >F_model = k_total * (F_calc + k_mask * F_mask) > > k_total = k_isotropic * k_anisotropic > Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso kani >kmask > 38.004-13.464 66.21 90 6 0.5449 232.778 190.690 0.824 0.739 >0.353 > 13.427-11.087 93.58 99 3 0.1952 *459.972 428.082 *1.279 0.749 >0.340 > 11.084-9.179 91.06 153 10 0.1983 502.739 469.985 1.271 0.749 >0.330 > 9.142-7.564 88.75 271 13 0.2210 405.976 376.935 1.215 0.751 >0.329 > 7.548-6.244 92.16 492 25 0.2733 342.193 302.079 1.212 0.751 >0.328 > 6.239-5.156 97.23 895 51 0.2545 365.657 321.767 1.164 0.750 >0.321 > 5.153-4.256 97.19 1575 83 0.1988 487.348 449.464 1.271 0.749 >0.270 > 4.256-3.514 99.83 2815 149 0.2169 582.502 526.163 1.702 0.748 >0.084 > 3.514-2.902 99.89 4989 263 0.2427 597.717 534.626 2.337 0.747 >0.060 > 2.901-2.396 99.85 8718 460 0.2988 532.605 456.384 2.752 0.744 >0.000 > 2.396-2.103 97.60 9284 494 0.3208 *546.159 458.454* 3.232 0.742 >0.000 > >So fix your data processing first - then your B factors should become >sensible and the R factors also - you are overweighting the high resolution >data greatly > > >And if the crystal is twinned the space group is actually P 32.. > >Cheers Eleanor > > > >On Wed, 28 May 2025 at 08:04, Janani Ganesh <[email protected]> wrote: > >> Dear Professor, >> >> Thank you for your response. I had tried out TLS as well to understand the >> trend, but it did not work. I am attaching the detwin and pointless log >> files for your reference. >> >> I even set the B-factors to an arbitrary value of 30 and performed >> refinement with overall B-factors, but there was no change in the B-factors >> at all. >> Is it possible for you to look at my data and help me with this issue? >> >> >> With my best regards, >> Janani Ganesh >> PhD Scholar, Protein Crystallography Section, >> Homi Bhabha National Institute, >> Mumbai, India. >> Contact No: +91-22-25594062 / +91-7506237778 >> > >######################################################################## > >To unsubscribe from the CCP4BB list, click the following link: 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